file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 35.0 38.0 39.0 39.1 41.0 42.0
## [1] 40
## [1] 35 35 37 37 37 37 37 37 38 38 38 38 38 38 39 39 39 39 39 39 39 39 39 39 39
## [26] 39 40 41 41 41 41 41 41 41 41 41 41 42 42 42
bioMart.All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]alias2Symbol function from
limma.a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}
table(is.na(a2s))##
## FALSE TRUE
## 1739 261
##
## FALSE TRUE <NA>
## 21 1718 261
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: LRRC6 DNAAF11
## 2: C11orf49 CSTPP1
## 3: LINC00476 ERCC6L2-AS1
## 4: HNRNPA1P48 HNRNPA1L3
## 5: ZRANB2-AS2 ZRANB2-DT
## 6: LINC00271 AHI1-DT
## 7: RFX3-AS1 RFX3-DT
## 8: LINC00884 ATP13A3-DT
## 9: FBXO30-DT EPM2A-DT
## 10: LINC00894 EOLA2-DT
## 11: COX10-AS1 COX10-DT
## 12: LINC01184 SLC12A2-DT
## 13: FAM198B-AS1 GASK1B-AS1
## 14: C5orf17 LINC02899
## 15: C8orf37-AS1 CFAP418-AS1
## 16: LINC01146 HISLA
## 17: BTBD11 ABTB3
## 18: H2BU1 H2BC26
## 19: SKIV2L SKIC2
## 20: FAM155A NALF1
## 21: CTB-41I6.2 PIK3R5-DT
## sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: CFTR CFTR CFTR
## 2: ICA1 ICA1 ICA1
## 3: PDK4 PDK4 PDK4
## 4: CALCR CALCR CALCR
## 5: ABCB4 ABCB4 ABCB4
## t1
## 1
## 2000
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp"
## reactome go_bp
## 1692 7647
Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: CFTR CFTR CFTR
## 2: ICA1 ICA1 ICA1
## [1] 36517 9
## gene_ids feature_is_filtered feature_name feature_reference
## 1: ENSG00000000003 FALSE TSPAN6 NCBITaxon:9606
## 2: ENSG00000000005 FALSE TNMD NCBITaxon:9606
## feature_biotype n_cells_by_counts mean_counts pct_dropout_by_counts
## 1: gene 76 0.002350 99.8100
## 2: gene 1 0.000025 99.9975
## total_counts
## 1: 94
## 2: 1
## [1] 2000
##
## TRUE
## 2000
##
## FALSE TRUE
## 34517 2000
gene_dat$selected = 0
gene_dat$selected[match(gene_info$sym_in_data, gene_dat$feature_name)] = 1
table(gene_dat$selected)##
## 0 1
## 34517 2000
## $`0`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 94.48 99.58 93.53 99.97 100.00
##
## $`1`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.6475 65.5944 84.3650 76.3053 93.6756 97.9950
gene_info = merge(gene_info, gene_dat, by.x="sym_in_data",
by.y="feature_name", all.x = TRUE, all.y = FALSE)
dim(gene_info)## [1] 2000 12
## sym_in_data sym_limma gene_symbol gene_ids feature_is_filtered
## 1: AATK AATK AATK ENSG00000181409 FALSE
## 2: ABAT ABAT ABAT ENSG00000183044 FALSE
## feature_reference feature_biotype n_cells_by_counts mean_counts
## 1: NCBITaxon:9606 gene 3157 0.091525
## 2: NCBITaxon:9606 gene 9074 0.368950
## pct_dropout_by_counts total_counts selected
## 1: 92.1075 3661 1
## 2: 77.3150 14758 1
max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol",
bias.data = 100 - gene_info$pct_dropout_by_counts)
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=81)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "CEACAM1" "HAMP" "DUOX1" "RAB40B"
## [5] "FOLR2" "ADGRG2" "FLJ40194" "DLEU7"
## [9] "FAM177B" "HNRNPA1P48" "EDNRB-AS1" "LINC01375"
## [13] "ENTPD1-AS1" "SLC8A1-AS1" "RP11-142M10.2" "SRGAP2-AS1"
## [17] "AC092431.3" "RNASEH2B-AS1" "RP11-353M9.1" "RP11-666F17.1"
## [21] "RP11-796E2.4" "FAM198B-AS1" "RP11-360F5.1" "AC006160.5"
## [25] "RP11-281P23.2" "RP11-238K6.1" "RP11-649G15.2" "RP11-452H21.1"
## [29] "RP11-513G19.1" "RP11-486A14.2" "RP11-136F16.1" "RP11-370I10.2"
## [33] "RP11-517O13.1" "ABHD15-AS1" "RP11-264E23.4" "RP11-7F3.1"
## [37] "AC009166.9" "RP11-56I23.2" "EME2"
## [1] 2
## [1] "OSBPL6" "P3H2" "GCNT2" "TENT5A" "RALGPS2" "NRN1"
## [7] "MIS18BP1" "KCNMB1" "AIG1" "SLC25A25" "MAGI1" "PTPN14"
## [13] "KCNMA1" "TIAM1" "TMEM169" "PLEKHA7" "NXN" "S100Z"
## [19] "MBOAT1" "SH3RF3" "NCKAP5" "APOO" "PLEKHA5" "RASSF2"
## [25] "MICU1" "DENND1A" "SLC35E1" "ZBTB46" "STARD13" "DENND4C"
## [31] "SLC12A6" "SRSF12" "AGAP1" "SLC43A2" "FAM110B" "TANC2"
## [37] "SIPA1L1"
## [1] 3
## [1] "ABCB4" "ARL5C" "AZIN2" "RASGEF1C"
## [5] "TMEM163" "GHRL" "GASK1B" "ADAMTS15"
## [9] "MICOS10" "MARCHF3" "PLCXD3" "KBTBD12"
## [13] "AC007879.5" "RP1-30E17.2" "CCDC26" "AC002539.1"
## [17] "LINC02642" "COX10-AS1" "LINC01141" "KCNMB2-AS1"
## [21] "LINC02008" "RP11-246A10.1" "XACT" "LINC02057"
## [25] "LINC01091" "AC008697.1" "LINC01094" "RP11-745L13.2"
## [29] "CTC-575N7.1" "MAILR" "SMIM35" "RP11-554D14.6"
## [33] "LINC02444" "RP11-588H23.3" "RP11-72M17.1" "RP11-399K21.11"
## [37] "LINC02712" "LINC01374" "RP11-692P14.1" "RP11-321P16.3"
## [41] "RP1-236J16.3"
## [1] 4
## [1] "BEX1" "ENPP3" "SLC9B1" "GPR85" "TCERG1L"
## [6] "WEE2-AS1" "AC011288.2" "COA6-AS1" "LINC00996" "ZNF528-AS1"
## [11] "TENM1" "FGF14" "ATP8A2" "STXBP5L" "TENM2"
## [16] "CNTN5" "ADGRL3" "ZNF385D" "SPOCK1" "AK5"
## [21] "NCAM2" "CAMK2N1" "GABRB1" "CSMD3" "LRFN5"
## [26] "NEGR1" "FUT9" "KCTD16" "FLRT2" "LSAMP"
## [31] "PTPRT" "TAFA2" "LINC00632" "FAM155A" "MEG3"
## [36] "RP11-191L9.4" "AC093843.1" "SHISA9" "RP11-384F7.2" "AGBL1"
## [41] "IQCJ-SCHIP1"
## [1] 5
## [1] "RBL1" "PRTFDC1" "DAAM1" "ARHGEF18" "ARSB"
## [6] "LRRC6" "ZSCAN5A" "MTHFS" "RALGPS1" "MAMDC2"
## [11] "ARHGAP42" "CDYL2" "LCLAT1" "SCAI" "LINC00476"
## [16] "C5orf64" "FIGN" "KIAA0825" "CENPP" "SCOC-AS1"
## [21] "RANBP17" "ATP6AP1L" "LIN52" "SLC16A1-AS1" "RP11-120D5.1"
## [26] "RORA-AS1" "LINC00506" "SNX25" "E2F3" "GABRG2"
## [31] "HELLS" "NR6A1" "GREM1" "FRMD3" "CDH4"
## [36] "SERTAD2" "SYCP2" "RP5-864K19.4" "CYP1B1-AS1" "HCG17"
## [41] "C2orf27A"
## [1] 6
## [1] "CELSR3" "ZNF365" "RBMS3"
## [4] "CLSTN2" "NRG2" "PRICKLE2"
## [7] "ARHGEF3" "RANBP3L" "ADGRV1"
## [10] "FSTL5" "HPSE2" "LRRC3B"
## [13] "POTEG" "CACNA1E" "ZNF521"
## [16] "LINC00970" "XKR9" "AC023469.1"
## [19] "ROR1-AS1" "SATB1-AS1" "LINC01435"
## [22] "RP11-147G16.1" "RP11-154D17.1" "AC013463.2"
## [25] "AC002066.1" "CTC-340A15.2" "USP2-AS1"
## [28] "RP11-696N14.1" "RP1-179N16.6" "LINC01609"
## [31] "RP11-661A12.5" "RMST" "RP11-20D14.3"
## [34] "RP11-396B14.2" "MTRNR2L12" "RMRP_ENSG00000269900"
## [37] "LINC00551" "CH507-513H4.1" "CH507-528H12.1"
## [40] "RP11-596C23.6" "RP4-799O8.1" "RP11-398J12.1"
## [1] 7
## [1] "SYNDIG1" "PLAT" "FAM149A" "TMEM156"
## [5] "ARMH4" "RP11-493L12.4" "ARHGAP6" "FSTL4"
## [9] "DDX3Y" "PILRA" "TGFB2" "GRK3"
## [13] "ITGB8" "SERPINE1" "BICRAL" "PADI2"
## [17] "OGFRL1" "CDH26" "TIAM2" "SLC2A13"
## [21] "DHRS13" "NCMAP" "GLDN" "CCDC73"
## [25] "NHEJ1" "ZNF846" "CYRIA" "ZDBF2"
## [29] "GCC2-AS1" "AC025171.1" "LNCAROD" "MYO16-AS1"
## [33] "FMN1" "RP11-351A11.1" "RP11-111A21.1" "RP11-707P17.1"
## [37] "RP11-358F13.1" "RP11-404C6.6" "RP11-452F19.4"
## [1] 8
## [1] "SIGLEC1" "PCSK1N" "MAP3K8" "FLVCR2"
## [5] "F13A1" "ENOSF1" "IFI44L" "CH25H"
## [9] "HERC6" "UBE2Q2" "FHAD1" "TMEM44"
## [13] "ADAMTS19" "ADGRA3" "BEX3" "MT1E"
## [17] "OLR1" "ODF3B" "H2BC4" "MX2"
## [21] "H2BC18" "TMSB4X" "MS4A4E" "RP11-123B3.2"
## [25] "RP5-1101C3.1" "ARHGAP8" "LINC01258" "LINC02196"
## [29] "ZNF10" "RP1-71H24.1" "OVCH1-AS1" "RP11-323I15.5"
## [33] "LINC01572" "RP11-386I14.4" "H2BC8" "H2AC8"
## [37] "RP11-736I24.5" "PLXNC1"
## [1] 9
## [1] "CALCR" "ZNF532"
## [3] "MBNL3" "OPHN1"
## [5] "MS4A4A" "ADGRG6"
## [7] "LDAH" "MTERF1"
## [9] "PIGC" "LRIG1"
## [11] "PSTPIP2" "PID1"
## [13] "RAB28" "PUS10"
## [15] "TMEM144" "DNAJC24"
## [17] "WDR25" "SDHAF3"
## [19] "PRDX6-AS1" "MAMDC2-AS1"
## [21] "ZNF433-AS1" "LINC00630"
## [23] "RPL34-DT" "LINC01278"
## [25] "RP11-195C7.1" "LINC02432"
## [27] "PVT1" "RP11-130F10.1"
## [29] "LIX1-AS1" "LINC01605_ENSG00000253161"
## [31] "LINC01146" "DISC1FP1"
## [33] "EIF1B-AS1" "RP11-323F24.5"
## [35] "RP4-545L17.11" "PARP8"
## [37] "IL15" "TMEM65"
## [39] "APLF" "KCNE1"
## [41] "ZNF407"
## [1] 10
## [1] "TPD52" "RPL3" "RPL18A" "RPL19" "RPL34"
## [6] "RPL24" "ATP5F1E" "FGF13" "RPS24" "PRDM5"
## [11] "RPS2" "RPS11" "RPL11" "SPAG16" "RPL32"
## [16] "FAU" "BEND6" "ATG10" "RPL26" "ELAVL4"
## [21] "MRPL1" "RPL38" "RPLP2" "RPS23" "SPATS2L"
## [26] "CPNE4" "RPL12" "RPL23A" "RPL39" "AIF1"
## [31] "DOK6" "SPOCK2" "SLC1A2" "ZMAT4" "LPL"
## [36] "ADARB1" "LILRB3" "SLC5A4-AS1"
## [1] 11
## [1] "DERA" "SNX24" "ITGA6" "POLA1" "MID1" "SUSD1"
## [7] "APBA1" "MAP2K6" "WLS" "AKAP7" "SLC10A7" "DTD1"
## [13] "METTL25" "LANCL2" "DPH6" "NPL" "IRF8" "MMS22L"
## [19] "NUBPL" "SAMSN1" "BACH1" "C1QC" "TNFRSF13C" "FILIP1L"
## [25] "SLC35G2" "C1QA" "PTPN2" "RTTN" "PROS1" "CCDC7"
## [31] "HGF" "FDFT1" "HACE1" "KLHL24" "COL5A1" "FNBP1L"
## [37] "GOLIM4"
## [1] 12
## [1] "NEXMIF" "NAV3" "CASS4" "PLCL1"
## [5] "GARNL3" "GIPC2" "UNC80" "TSPAN7"
## [9] "CACNA1D" "RNF180" "CCDC171" "NAV2"
## [13] "ZNF608" "MACROD2" "KCNIP1" "ERC2"
## [17] "COL25A1" "ALOX12-AS1" "LINC00539" "RP11-535M15.1"
## [21] "STX18-AS1" "LINC02232" "MRPS30-DT" "RP4-809F18.1"
## [25] "RP11-370I10.6" "RP11-622O11.6" "COPG2IT1" "RP11-640F22.1"
## [29] "RP11-320L2.1" "DOCK3" "CUX2" "WDR45B"
## [33] "KCND3" "DPP10" "ANKS1B" "KCNIP4"
## [37] "AIDA" "RYR2" "SNHG14"
## [1] 13
## [1] "MCF2L2" "CYFIP2" "CST3" "STS" "ABCC4" "DOCK10"
## [7] "BCAS3" "FOXO1" "BTG2" "ANO10" "ARHGAP25" "B2M"
## [13] "BTD" "SERPINB9" "XKR6" "DYNC2H1" "RPL41" "RORA"
## [19] "SLC1A3" "DOCK9" "PRKAG2" "RAPGEF1" "PTPRE" "SSH2"
## [25] "SDK1" "MGAT5" "FMNL2" "RUNX1" "CLASP2" "OXR1"
## [31] "LDLRAD4" "GPHN" "CEBPB" "CHD2" "BAIAP2" "MYO1D"
## [37] "PCDH9" "GDI1" "NEAT1"
## [1] 14
## [1] "TNFRSF21" "JARID2" "ARAP2" "CPSF1" "GRAMD4" "PPP1R15A"
## [7] "CEP170B" "TBL1X" "INTS6" "HSF4" "UBE2R2" "DNAJC12"
## [13] "DCUN1D4" "BBX" "CYTIP" "TSHZ3" "MGAT1" "PHF21A"
## [19] "IQGAP2" "GFOD1" "GNA12" "THRB" "RPP38" "CAMK4"
## [25] "RASSF3" "ASAP1" "RASA2" "CDC42SE2" "SLMAP" "STXBP5"
## [31] "PCDH7" "SH3PXD2B" "CMSS1" "ARL4C" "RALGAPA2" "IARS1"
## [37] "ZNF277" "EFCAB2" "ZSCAN31"
## [1] 15
## [1] "LRRC74A" "MEIS1" "ZNF707" "HECW1" "PKD1"
## [6] "NCDN" "PTPRN" "ITPKC" "PCSK5" "FLT1"
## [11] "EPHA4" "KDM5B" "NR4A3" "ZC4H2" "AFDN"
## [16] "EMILIN2" "RAMP1" "MACROD1" "MICAL2" "KCNK1"
## [21] "CRIM1" "NPAS3" "CACNA2D1" "PTPRN2" "SORCS3"
## [26] "PALM2AKAP2" "FGF17" "SPTBN4" "UNC5C" "TSHZ2"
## [31] "NELL2" "ZBTB7C" "PBX1" "MIB2" "SLC48A1"
## [36] "MTRNR2L1" "GRIN2B"
## [1] 16
## [1] "PRKCQ" "FOXP2" "ATF5" "XIST" "GCLC"
## [6] "GCLM" "PRKCH" "WWC3" "ZFAT" "MYO9A"
## [11] "ARHGAP15" "ANKRD12" "ADAP1" "MEGF9" "FOXP1"
## [16] "SEM1" "KIAA0513" "CAMKMT" "FER" "RASGRP3"
## [21] "MERTK" "JAZF1" "ADK" "ST3GAL2" "EPB41"
## [26] "FBXO27" "NEK10" "MTSS1" "MALT1" "FUT10"
## [31] "RESF1" "SLC35E3" "SAMD12" "CSMD1" "MAML2"
## [36] "NPIPB15" "CARD11" "SOGA3" "AC092835.2"
## [1] 17
## [1] "ADGRD1" "PDE10A" "NEURL2" "BANK1"
## [5] "ADAMTS3" "UCN" "PGBD5" "TMEM151B"
## [9] "HDAC4-AS1" "RP11-445F6.2" "SMCR5" "LINC01515"
## [13] "LINC01277" "RP3-525N10.2" "LINC00271" "LINC02884"
## [17] "AC007682.1" "RP11-142A5.1" "AC073115.6" "BDNF-AS"
## [21] "LINC02211" "RP11-115J16.1" "C5orf17" "RP11-673E1.1"
## [25] "LINC02055" "FAM66D" "MIR100HG" "PRANCR"
## [29] "CTD-2336H13.2" "LINC02073" "CCDC28A-AS1" "RP11-413N10.3"
## [33] "CERNA2" "RP11-221G19.1" "LINC02885" "RP11-237N2.1"
## [37] "RP11-38B6.1" "RP13-52K8.2"
## [1] 18
## [1] "OSBPL5" "SNCAIP"
## [3] "MGLL" "RPH3A"
## [5] "GDAP1" "CD69"
## [7] "PDE4D" "ZRANB3"
## [9] "CHN1" "CALY"
## [11] "EFCAB11" "RNF157"
## [13] "NRGN" "ABCA5"
## [15] "CPLX1" "KCNMB2"
## [17] "ALG1L9P_ENSG00000248671" "CEROX1"
## [19] "ADAM22" "VCAN"
## [21] "PDE4A" "KCNAB2"
## [23] "RAB27A" "ZNF586"
## [25] "NCS1" "SASH1"
## [27] "HPCAL1" "SH3BP5"
## [29] "SNAP25" "PAM"
## [31] "MSI2" "STARD9"
## [33] "KALRN" "MSRA"
## [35] "CADM1" "PDE4B"
## [37] "KAZN" "UNC13B"
## [39] "MICAL3"
## [1] 19
## [1] "ETV1" "SCMH1" "IGF1" "PER3" "APBB1IP" "IL1A"
## [7] "IL1B" "IL6ST" "SLC22A23" "TRPC1" "MLIP" "COPG2"
## [13] "NLRP3" "KIF26B" "SFMBT1" "TMEM52B" "DTWD2" "DENND5B"
## [19] "DLEU1" "SLC8A1" "PRKN" "SFMBT2" "MBD5" "LTC4S"
## [25] "LIPE-AS1" "MIR99AHG" "MATK" "RNASET2" "RBFOX1" "PDGFB"
## [31] "LIFR" "HPCAL4" "SLC6A8" "SLC2A5" "FAT3" "RBFOX3"
## [37] "TNFRSF10C" "PCGF5"
## [1] 20
## [1] "ZFP64" "EFR3B" "EPDR1" "TXNDC16"
## [5] "PARD3B" "GALNT12" "IFT43" "SIRPD"
## [9] "FBN2" "TEX9" "LINC00467" "DISP1"
## [13] "CLIC2" "MAP3K7CL" "AIM2" "ATF7IP2"
## [17] "TMC7" "SPTLC3" "RAB39A" "FSIP2"
## [21] "LEKR1" "LINC01356" "AC097721.2" "RP5-1198O20.4"
## [25] "FSIP2-AS1" "RP11-634B7.4" "CDKN2B-AS1" "LINC00968"
## [29] "STARD4-AS1" "RP11-120A1.1" "RP11-10H3.1" "MIR3142HG"
## [33] "RHOXF1-AS1" "LINC02666" "RP1-111C20.3" "GALNT18"
## [37] "ARHGEF25" "CPEB2-DT" "CTB-41I6.2"
## [1] 21
## [1] "ERCC8" "OXCT1" "ALDOC" "CCDC18" "DSTN" "PIGK" "IER2"
## [8] "BACE2" "ABAT" "CDK14" "CDK17" "TGFBR3" "PGM1" "NPDC1"
## [15] "TPI1" "SOD2" "PAPOLG" "HSPH1" "CAMK1" "DNAJB2" "UACA"
## [22] "CPNE8" "MSN" "MCPH1" "CFDP1" "PTMS" "PCNT" "GLRX"
## [29] "AGFG1" "FAM20C" "ZDHHC20" "LIMK2" "COL27A1" "HSPA1B" "PPME1"
## [1] 22
## [1] "ACKR4" "HIVEP2" "MAMLD1" "HDHD5"
## [5] "MAP3K20" "GADD45B" "IL4I1" "LILRB5"
## [9] "HS3ST2" "TREM1" "GPNMB" "NIBAN2"
## [13] "RASGEF1B" "TAMALIN" "IER5" "ATOH8"
## [17] "VMO1" "ADSS1" "ANKRD37" "ZNF395"
## [21] "TPRG1" "H2BU1" "AF064858.6" "AS3MT"
## [25] "FAM229A" "LIMD1-AS1" "DIRC3" "DARS1-AS1"
## [29] "RP11-47I22.3" "AC009505.4" "MIR155HG" "AF064858.8"
## [33] "SELENOP" "LINC02698" "CLEC5A" "SAP30-DT"
## [37] "MYOCOS" "RP11-475M20.2" "CTD-2285E13.1" "RENO1"
## [41] "RP11-134L10.2"
## [1] 23
## [1] "RIPOR2" "LILRB2" "MCTP2" "ABCA8"
## [5] "MTHFD2L" "RAB37" "ARSJ" "CARNMT1-AS1"
## [9] "PCDH9-AS2" "AC073115.7" "TRG-AS1" "RP11-341N18.1"
## [13] "RP11-120L14.1" "GALNT16" "CDH20" "MYOM1"
## [17] "KATNAL1" "STN1" "ARFGEF3" "ADAM23"
## [21] "MXI1" "ATP8A1" "PCSK2" "PATJ"
## [25] "BTBD11" "PITPNC1" "FBXO32" "ZFYVE28"
## [29] "JAML" "PLPP3" "SNED1" "AMER2"
## [33] "KLF13" "TBC1D10C" "JAKMIP2" "ZHX2"
## [37] "TMTC2" "SSTR2" "CD247" "CCDC71L"
## [41] "LINC01138"
## [1] 24
## [1] "RASGRP2" "FAM50A"
## [3] "ADGRL1" "SLC26A3"
## [5] "AK1" "DRAM1"
## [7] "CCNG2" "PGGHG"
## [9] "PXDNL" "LRRC4C"
## [11] "CLEC1A" "AMN1"
## [13] "CFAP161" "TNFRSF11B"
## [15] "SEMA3E" "LPCAT4"
## [17] "LINC00910" "LINC00862"
## [19] "LINC02397" "C17orf67"
## [21] "LINC01320" "ARL17B"
## [23] "KLF3-AS1" "SGO1-AS1"
## [25] "AC067959.1" "LINC01762"
## [27] "RP3-467L1.4" "LINC02646"
## [29] "RP11-305L7.3" "RP11-657O9.1"
## [31] "LINC01322" "RP11-17A1.3"
## [33] "RP11-79E3.2" "RP11-81K2.1"
## [35] "SCARNA2_ENSG00000270066" "RP11-154H23.4"
## [37] "RP11-114N19.3" "RP11-344F5.1"
## [39] "AC003099.2"
## [1] 25
## [1] "MPP2" "IRAK1BP1" "SKA2" "CNTN1" "LRRC7" "CTNNA2"
## [7] "ZFY" "ARHGAP10" "RAPGEF4" "CELF4" "KCNT1" "CPE"
## [13] "MOB3B" "OLFM1" "PDZD2" "KCNH1" "CDH18" "CNKSR2"
## [19] "ME3" "SCN3A" "FMN2" "SYN2" "EDIL3" "NLGN1"
## [25] "CTNND2" "DLGAP1" "C11orf80" "CNTNAP2" "PPM1E" "RIMS2"
## [31] "NRXN1" "OPCML" "RALYL" "OSBP2" "PRKG1" "SYN3"
## [37] "MYT1L" "MAGI2" "GRM7"
## [1] 26
## [1] "ADAM28" "PROCR" "NEK11" "CCDC170" "SMAD6" "MED12L" "SAMD4A"
## [8] "NSMAF" "LIMCH1" "PHLPP1" "IRAK3" "FKBP5" "USP9Y" "FOXO3"
## [15] "ELL2" "RUNX2" "DOCK6" "ZNF331" "IRAK2" "CCNH" "NHSL1"
## [22] "FAM117B" "FAM13A" "PELI2" "MAP3K6" "USP53" "NEK7" "PDE3B"
## [29] "OTUD1" "LRP1B" "PPIP5K1" "BNC2" "H2AC6" "GPRIN3" "SULF2"
## [36] "PELI1" "CEBPD"
## [1] 27
## [1] "IPCEF1" "PEX7" "ITPR2" "C3" "STAMBPL1"
## [6] "GSTCD" "FRMD6" "ITGA9" "TBC1D32" "FRMD4A"
## [11] "LRRC8C" "ZMAT3" "ATAD5" "CA8" "SLC9A9"
## [16] "CACNB4" "MEI4" "SCIN" "CLEC16A" "LCP2"
## [21] "PAG1" "CTTNBP2" "RFX3" "RFX2" "RASSF8"
## [26] "ARHGAP22" "PRAM1" "WNT2B" "GYPC" "CSGALNACT1"
## [31] "DIXDC1" "SH3RF1" "DHRSX" "PACS1" "FADS3"
## [1] 28
## [1] "PKD2L2" "IL7" "SGCE" "MIR4435-2HG"
## [5] "GLIPR1L1" "TTTY14" "MCMDC2" "EYS"
## [9] "RP1-225E12.2" "RP5-1132H15.1" "LANCL1-AS1" "ITGA9-AS1"
## [13] "RMDN2-AS1" "LRIG2-DT" "RP11-775D22.3" "RP11-544A12.8"
## [17] "RP11-506H20.1" "RP11-1H15.2" "RP11-867G2.8" "RP11-571M6.7"
## [21] "RP11-160E2.6" "RP11-703M24.5" "CEACAM16-AS1" "KCNQ1OT1"
## [25] "RP11-74J13.8" "RP11-305E17.8" "RP11-793H13.14" "RP1-18C9.3"
## [29] "RP11-65F13.4" "RP11-13J12.3" "RP11-6G22.1" "RP11-685G9.5"
## [33] "RP11-555K12.4" "RP11-617F9.2" "ST3GAL1" "SLC9A7"
## [37] "PCDH11Y" "APBB3" "H1-10" "RP11-37N22.1"
## [41] "RP11-384C4.7" "RP11-322M13.1"
## [1] 29
## [1] "PLPP1" "ACER3" "SP140" "CARMIL1"
## [5] "ZNF821" "RCAN3" "PLAGL1" "SSPN"
## [9] "PUDP" "SPATA6" "TBC1D14" "EPHB2"
## [13] "ARHGAP20" "SLC49A4" "NKD1" "WDPCP"
## [17] "C11orf49" "CD226" "DENND2B" "FGGY"
## [21] "B3GNT5" "PCED1B" "SCFD2" "FIRRE"
## [25] "LINC02649" "FTCDNL1" "RP11-162D16.2" "RP11-202G18.1"
## [29] "RFX3-AS1" "RP11-557H15.4" "LINC00884" "LINC01184"
## [33] "LINC02762" "LINC02328" "RP11-154H12.3" "TSIX"
## [37] "RP11-323P17.2" "MIR223HG" "RP11-419I17.1" "SEC14L1"
## [1] 30
## [1] "HTR2B" "TAGAP" "PNMA3" "TWIST2" "NFIX"
## [6] "TNS1" "RNF24" "RNMT" "BNIP3L" "GYS1"
## [11] "ARRDC2" "GBE1" "RLF" "SPP1" "IQSEC2"
## [16] "SOX5" "IQSEC1" "SLC25A37" "RIT2" "AGPAT5"
## [21] "MAPK13" "SSBP3" "ETS2" "ABCG1" "ABCA1"
## [26] "DDIT4" "SNTB2" "CRADD" "PPP1R3B" "BNIP3"
## [31] "FAM210A" "CHST15" "H1-0" "RGL3" "AC093818.1"
## [36] "RP11-13N12.1" "FMNL1-DT"
## [1] 31
## [1] "PDK4" "NLRP1" "CPED1" "PEBP4"
## [5] "GPAT3" "CFAP74" "GASK1A" "TENM4"
## [9] "SETBP1" "C4orf19" "DEPTOR" "MIR31HG"
## [13] "CYSLTR1" "KCNQ3" "RTN4RL1" "CLEC9A"
## [17] "LINC01285" "RP11-131L23.1" "LINC01357" "AC105760.2"
## [21] "KIF9-AS1" "HDAC2-AS2" "HMGA1P4" "MIR4300HG"
## [25] "CTB-161M19.4" "ZFPM2-AS1" "LINC01301" "RP11-946L16.1"
## [29] "RP11-187O7.3" "MRC1" "ATP6V0D1-DT" "RP11-495L19.1"
## [33] "RP11-437L7.2" "RP11-168F24.3" "RP11-4F5.3" "KCNQ2"
## [37] "HTR1E" "KCNQ5" "RP11-249L21.6"
## [1] 32
## [1] "TTC7A" "NIPAL2"
## [3] "GAREM1" "SESN3"
## [5] "PLXDC1" "HESX1"
## [7] "NMNAT3" "LIPC"
## [9] "PLD4" "CX3CR1"
## [11] "ACYP2" "ZDHHC14"
## [13] "CATSPERE" "SPATA13_ENSG00000182957"
## [15] "RNLS" "B3GLCT"
## [17] "AC003090.1" "ENTPD3-AS1"
## [19] "TMEM72-AS1" "CTA-292E10.6"
## [21] "TEX41" "LMCD1-AS1"
## [23] "RP13-188A5.1" "MIR646HG"
## [25] "HCG22" "ZRANB2-AS2"
## [27] "LINC01376" "RNF217-AS1"
## [29] "MEF2C-AS1" "RP11-319G6.1"
## [31] "RP11-381K20.2" "RP11-692D12.1"
## [33] "GMDS-DT" "RP11-679C8.2"
## [35] "C8orf37-AS1" "RP11-541P9.3"
## [37] "RP11-511B23.2" "LINC00907"
## [39] "MIR222HG" "RP11-111G13.1"
## [41] "RP11-685G11.1"
## [1] 33
## [1] "MUSK" "ANGPT2" "ECM2" "FMO5" "BCL2A1"
## [6] "ZDHHC19" "BEAN1" "GLYATL1" "MOBP" "RP11-621L6.2"
## [11] "SLC2A3" "ABCA7" "PLEKHH3" "ANO8" "RAP1GAP"
## [16] "HIF3A" "CHI3L1" "BTG1" "CEMIP2" "HILPDA"
## [21] "ADCY3" "RGS16" "TMEM140" "ST18" "PLIN2"
## [26] "LYPD5" "CCDC107" "ANKZF1" "NFIL3" "ALDH1A1"
## [31] "ADCY5" "RBM44" "CD55" "ERO1A" "SH3BGRL2"
## [36] "STARD10" "SLC12A8" "HIF1A-AS3"
## [1] 34
## [1] "ATP8B1" "SLC5A9" "SHOC1" "ENO4"
## [5] "INSYN2B" "ANKUB1" "AC002463.3" "ELMO1-AS1"
## [9] "TMLHE-AS1" "AC096558.1" "RP4-568F9.6" "AC083884.8"
## [13] "AC037445.1" "CPB2-AS1" "MYCBP2-AS1" "DIAPH2-AS1"
## [17] "CCDC200" "AC018890.6" "LINC01877" "MEF2C-AS2"
## [21] "CTD-2015H6.3" "RHOQ-AS1" "RP11-268P4.5" "AP000487.6"
## [25] "RP11-638I2.8" "LINC02316" "USP3-AS1" "RP11-815J21.4"
## [29] "RP11-16B9.1" "PRKCA-AS1" "RP11-16C1.3" "RP11-793A3.2"
## [33] "RP11-58G13.1" "RP1-256G22.2" "CTD-2282P23.2" "DISC2"
## [37] "RP11-314L11.1" "RP11-261A24.1" "RP11-1H15.4" "RP11-1146N6.3"
## [41] "SLC26A7"
## [1] 35
## [1] "HHAT" "XAF1" "FBXL13" "PAQR3" "LINC00624"
## [6] "MSR1" "PDE8A" "RGS1" "DARS1" "GTDC1"
## [11] "SRGN" "RGL1" "MYO10" "TNFAIP8" "ARHGAP18"
## [16] "RSU1" "HTR7" "ARID5B" "NGLY1" "ACSL1"
## [21] "FRRS1" "ACOT11" "CDCP1" "RHOBTB3" "MARCHF8"
## [26] "ALCAM" "KLHL6" "MFSD4B" "TNFAIP8L3" "MITF"
## [31] "DPYD" "PARVB" "CTD-3088G3.8" "UBXN2B" "PIK3IP1-DT"
## [36] "MIR181A1HG" "CTD-2643I7.5" "IFITM10" "SBF2-AS1"
## [1] 36
## [1] "CRYM" "IGSF11" "GLT1D1" "TSBP1-AS1"
## [5] "KIF5C-AS1" "MEIKIN" "MTRNR2L8" "PSMD7-DT"
## [9] "SYT7" "COL5A3" "IGSF9B" "NALCN"
## [13] "DNAH6" "CHD5" "CSMD2" "CBLN2"
## [17] "CFAP251" "PDZRN4" "STXBP6" "CXXC5"
## [21] "CADM2" "SRRM3" "ADGRB1" "NRG3"
## [25] "SLIT1" "CR1L" "RORB" "FAM153CP"
## [29] "BASP1-AS1" "MIAT" "TRHDE-AS1" "RP11-259O2.1"
## [33] "LINC01414" "CTC-535M15.2" "RP11-429A20.3" "RP11-368L12.1"
## [37] "LINC00558" "U91319.1" "RP11-436D23.1" "RP5-1015P16.1"
## [41] "RP11-335E8.3"
## [1] 37
## [1] "ICA1" "PRDM11" "ST6GAL1" "SLC26A4"
## [5] "PODXL2" "AOPEP" "LY96" "SMIM14"
## [9] "PRMT9" "GPR34" "GAP43" "CAPS2"
## [13] "CDIN1" "SRGAP3" "CHSY3" "C12orf75"
## [17] "LINC00894" "LINC01684" "RP11-37B2.1" "RP11-630C16.2"
## [21] "RP11-574F11.4" "STAB1" "SESN1" "TMED8"
## [25] "IL27RA" "NCOA7" "FRMD4B" "TMEM115"
## [29] "CHSY1" "SLC41A2" "TLR2" "DHRS3"
## [33] "ROBO1" "RNF150" "LONRF3" "TRNAU1AP"
## [37] "TLR5" "ZC3H6"
## [1] 38
## [1] "CECR2" "NME3" "ABCC1" "OGN" "PLGRKT"
## [6] "IFIT3" "IFIT2" "CENPK" "SAT1" "RTN4IP1"
## [11] "PCBD2" "ITM2C" "ERMN" "TET1" "LPAR6"
## [16] "PTH2R" "ADGRG5" "FAM227B" "RIC3" "TLN2"
## [21] "NAALADL2" "ZFP36L1" "IFIT1" "DNAH14" "ZNRF1"
## [26] "CH17-55D9.1" "RP6-91H8.6" "RP4-681L3.3" "ATP9A" "RGCC"
## [31] "TGFBI" "ATP8B2" "KIF5C" "KLC2" "MAMDC4"
## [36] "IFNLR1" "GK"
## [1] 39
## [1] "PLEK" "CYREN" "RAB38" "MMP24"
## [5] "OMD" "TMEM241" "IER3" "AGBL3"
## [9] "NLGN4Y" "CYTL1" "IRAG1-AS1" "H2AC20"
## [13] "AC023590.1" "ARHGAP26-AS1" "ZNF451-AS1" "AC105461.1"
## [17] "ALG13-AS1" "ARHGAP15-AS1" "IPO9-AS1" "RAP2C-AS1"
## [21] "UFL1-AS1" "RP11-528G1.2" "FBXO30-DT" "KDM4A-AS1"
## [25] "BCL2L1-AS1" "RP11-544A12.4" "DENND6A-AS1" "ZBTB20-AS5"
## [29] "GPRC5D-AS1" "RP11-434H14.1" "LINC00639" "RP11-106M3.3"
## [33] "RNF213-AS1" "H2BC7" "RP11-121C2.3" "RP11-19D22.1"
## [37] "RP11-622I12.1" "RP11-458A7.1" "RP11-21M24.6" "RP11-314E10.1"
## [41] "RP11-399K19.1"
## [1] 40
## [1] "ANGPTL1" "C11orf65" "COL5A2" "SPDYE2"
## [5] "MTCP1" "RP11-321C24.1" "DOCK4-AS1" "RP11-165F24.3"
## [9] "AC017101.10" "RP11-526K17.2" "RP11-575L7.8" "RP1-117O3.2"
## [13] "KCNMA1-AS1" "LINC00960" "RP11-712B9.2" "ANK2-AS1"
## [17] "CTD-2227I18.1" "LINC02742" "RP11-39E3.3" "CTD-3239E11.2"
## [21] "RP11-624C23.1" "RP11-463D19.1" "CTD-2537O9.1" "RP11-493L12.3"
## [25] "RP11-713N11.4" "CTD-2647E9.3" "RP11-317G6.1" "RP11-516C1.1"
## [29] "LMO7-AS1" "RP11-66H6.3" "LINC00621" "RP11-737O24.2"
## [33] "TCF4-AS1" "RP11-53B2.3" "RP11-126O1.4" "CTD-3149D2.4"
## [37] "RP4-769N13.7" "H2AC19" "RP11-275G7.2" "GS1-98E2.1"
## [41] "RP1-80B9.4" "CTD-2021K4.2"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_8"
## [1] "SIGLEC1" "PCSK1N" "MAP3K8" "FLVCR2"
## [5] "F13A1" "ENOSF1" "IFI44L" "CH25H"
## [9] "HERC6" "UBE2Q2" "FHAD1" "TMEM44"
## [13] "ADAMTS19" "ADGRA3" "BEX3" "MT1E"
## [17] "OLR1" "ODF3B" "H2BC4" "MX2"
## [21] "H2BC18" "TMSB4X" "MS4A4E" "RP11-123B3.2"
## [25] "RP5-1101C3.1" "ARHGAP8" "LINC01258" "LINC02196"
## [29] "ZNF10" "RP1-71H24.1" "OVCH1-AS1" "RP11-323I15.5"
## [33] "LINC01572" "RP11-386I14.4" "H2BC8" "H2AC8"
## [37] "RP11-736I24.5" "PLXNC1"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 412 hats acetylate histones 4.170912e-05 0.9999991
## 415 hcmv late events 6.723915e-05 0.9999982
## 416 hdacs deacetylate histones 7.108510e-05 0.9999981
## numDEInCat numInCat FDR
## 412 4 9 0.02800753
## 415 4 11 0.02800753
## 416 4 11 0.02800753
##
## [1] "set_10"
## [1] "TPD52" "RPL3" "RPL18A" "RPL19" "RPL34"
## [6] "RPL24" "ATP5F1E" "FGF13" "RPS24" "PRDM5"
## [11] "RPS2" "RPS11" "RPL11" "SPAG16" "RPL32"
## [16] "FAU" "BEND6" "ATG10" "RPL26" "ELAVL4"
## [21] "MRPL1" "RPL38" "RPLP2" "RPS23" "SPATS2L"
## [26] "CPNE4" "RPL12" "RPL23A" "RPL39" "AIF1"
## [31] "DOK6" "SPOCK2" "SLC1A2" "ZMAT4" "LPL"
## [36] "ADARB1" "LILRB3" "SLC5A4-AS1"
## $reactome
## category over_represented_pvalue
## 138 cellular response to starvation 0
## 301 eukaryotic translation elongation 0
## 302 eukaryotic translation initiation 0
## 452 influenza infection 0
## 557 metabolism of amino acids and derivatives 0
## 640 nonsense mediated decay nmd 0
## 801 regulation of expression of slits and robos 0
## 850 response of eif2ak4 gcn2 to amino acid deficiency 0
## 901 rrna processing 0
## 927 selenoamino acid metabolism 0
## under_represented_pvalue numDEInCat numInCat FDR
## 138 1 18 26 0
## 301 1 18 23 0
## 302 1 18 23 0
## 452 1 18 27 0
## 557 1 18 41 0
## 640 1 18 23 0
## 801 1 18 27 0
## 850 1 18 25 0
## 901 1 18 25 0
## 927 1 18 26 0
##
## $go_bp
## category over_represented_pvalue
## 630 cytoplasmic translation 0.000000e+00
## 4283 ribosome biogenesis 2.296868e-10
## 4279 ribosomal large subunit biogenesis 1.498704e-08
## 4278 ribosomal large subunit assembly 5.811626e-07
## 4281 ribosomal small subunit biogenesis 2.783323e-06
## 4282 ribosome assembly 2.822337e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 630 1 18 23 0.000000e+00
## 4283 1 8 13 5.420610e-07
## 4279 1 5 5 2.357960e-05
## 4278 1 4 4 6.857719e-04
## 4281 1 4 5 2.220238e-03
## 4282 1 4 5 2.220238e-03
##
## [1] "set_12"
## [1] "NEXMIF" "NAV3" "CASS4" "PLCL1"
## [5] "GARNL3" "GIPC2" "UNC80" "TSPAN7"
## [9] "CACNA1D" "RNF180" "CCDC171" "NAV2"
## [13] "ZNF608" "MACROD2" "KCNIP1" "ERC2"
## [17] "COL25A1" "ALOX12-AS1" "LINC00539" "RP11-535M15.1"
## [21] "STX18-AS1" "LINC02232" "MRPS30-DT" "RP4-809F18.1"
## [25] "RP11-370I10.6" "RP11-622O11.6" "COPG2IT1" "RP11-640F22.1"
## [29] "RP11-320L2.1" "DOCK3" "CUX2" "WDR45B"
## [33] "KCND3" "DPP10" "ANKS1B" "KCNIP4"
## [37] "AIDA" "RYR2" "SNHG14"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 113 cardiac conduction 2.383914e-05 0.9999995
## 599 muscle contraction 5.461467e-05 0.9999986
## numDEInCat numInCat FDR
## 113 4 18 0.02817787
## 599 4 24 0.03227727
##
## [1] "set_16"
## [1] "PRKCQ" "FOXP2" "ATF5" "XIST" "GCLC"
## [6] "GCLM" "PRKCH" "WWC3" "ZFAT" "MYO9A"
## [11] "ARHGAP15" "ANKRD12" "ADAP1" "MEGF9" "FOXP1"
## [16] "SEM1" "KIAA0513" "CAMKMT" "FER" "RASGRP3"
## [21] "MERTK" "JAZF1" "ADK" "ST3GAL2" "EPB41"
## [26] "FBXO27" "NEK10" "MTSS1" "MALT1" "FUT10"
## [31] "RESF1" "SLC35E3" "SAMD12" "CSMD1" "MAML2"
## [36] "NPIPB15" "CARD11" "SOGA3" "AC092835.2"
## $reactome
## category over_represented_pvalue
## 314 fceri mediated nf kb activation 1.618734e-05
## 391 glutathione conjugation 1.308212e-04
## 392 glutathione synthesis and recycling 1.308212e-04
## 555 metabolic disorders of biological oxidation enzymes 1.308212e-04
## 258 downstream signaling events of b cell receptor bcr 1.341146e-04
## under_represented_pvalue numDEInCat numInCat FDR
## 314 0.9999997 4 8 0.01913344
## 391 1.0000000 2 2 0.03170469
## 392 1.0000000 2 2 0.03170469
## 555 1.0000000 2 2 0.03170469
## 258 0.9999958 4 10 0.03170469
##
## [1] "set_18"
## [1] "OSBPL5" "SNCAIP"
## [3] "MGLL" "RPH3A"
## [5] "GDAP1" "CD69"
## [7] "PDE4D" "ZRANB3"
## [9] "CHN1" "CALY"
## [11] "EFCAB11" "RNF157"
## [13] "NRGN" "ABCA5"
## [15] "CPLX1" "KCNMB2"
## [17] "ALG1L9P_ENSG00000248671" "CEROX1"
## [19] "ADAM22" "VCAN"
## [21] "PDE4A" "KCNAB2"
## [23] "RAB27A" "ZNF586"
## [25] "NCS1" "SASH1"
## [27] "HPCAL1" "SH3BP5"
## [29] "SNAP25" "PAM"
## [31] "MSI2" "STARD9"
## [33] "KALRN" "MSRA"
## [35] "CADM1" "PDE4B"
## [37] "KAZN" "UNC13B"
## [39] "MICAL3"
## $reactome
## category over_represented_pvalue
## 203 darpp 32 events 0.0000162074
## 6 acetylcholine neurotransmitter release cycle 0.0001171809
## 641 norepinephrine neurotransmitter release cycle 0.0001171809
## under_represented_pvalue numDEInCat numInCat FDR
## 203 1.0000000 3 3 0.01915715
## 6 0.9999988 3 5 0.04616926
## 641 0.9999988 3 5 0.04616926
##
## [1] "set_19"
## [1] "ETV1" "SCMH1" "IGF1" "PER3" "APBB1IP" "IL1A"
## [7] "IL1B" "IL6ST" "SLC22A23" "TRPC1" "MLIP" "COPG2"
## [13] "NLRP3" "KIF26B" "SFMBT1" "TMEM52B" "DTWD2" "DENND5B"
## [19] "DLEU1" "SLC8A1" "PRKN" "SFMBT2" "MBD5" "LTC4S"
## [25] "LIPE-AS1" "MIR99AHG" "MATK" "RNASET2" "RBFOX1" "PDGFB"
## [31] "LIFR" "HPCAL4" "SLC6A8" "SLC2A5" "FAT3" "RBFOX3"
## [37] "TNFRSF10C" "PCGF5"
## $go_bp
## category over_represented_pvalue
## 2767 positive regulation of mitotic nuclear division 1.062274e-06
## 2818 positive regulation of nuclear division 1.062274e-06
## 3678 regulation of mitotic nuclear division 1.878468e-06
## 3750 regulation of nuclear division 1.878468e-06
## 37 acute inflammatory response 4.198804e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 2767 1.0000000 4 7 0.002216593
## 2818 1.0000000 4 7 0.002216593
## 3678 1.0000000 4 8 0.002216593
## 3750 1.0000000 4 8 0.002216593
## 37 0.9999991 4 8 0.039636712
##
## [1] "set_26"
## [1] "ADAM28" "PROCR" "NEK11" "CCDC170" "SMAD6" "MED12L" "SAMD4A"
## [8] "NSMAF" "LIMCH1" "PHLPP1" "IRAK3" "FKBP5" "USP9Y" "FOXO3"
## [15] "ELL2" "RUNX2" "DOCK6" "ZNF331" "IRAK2" "CCNH" "NHSL1"
## [22] "FAM117B" "FAM13A" "PELI2" "MAP3K6" "USP53" "NEK7" "PDE3B"
## [29] "OTUD1" "LRP1B" "PPIP5K1" "BNC2" "H2AC6" "GPRIN3" "SULF2"
## [36] "PELI1" "CEBPD"
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 4565 toll signaling pathway 9.170054e-06 0.9999999
## numDEInCat numInCat FDR
## 4565 4 5 0.04328265
##
## [1] "set_31"
## [1] "PDK4" "NLRP1" "CPED1" "PEBP4"
## [5] "GPAT3" "CFAP74" "GASK1A" "TENM4"
## [9] "SETBP1" "C4orf19" "DEPTOR" "MIR31HG"
## [13] "CYSLTR1" "KCNQ3" "RTN4RL1" "CLEC9A"
## [17] "LINC01285" "RP11-131L23.1" "LINC01357" "AC105760.2"
## [21] "KIF9-AS1" "HDAC2-AS2" "HMGA1P4" "MIR4300HG"
## [25] "CTB-161M19.4" "ZFPM2-AS1" "LINC01301" "RP11-946L16.1"
## [29] "RP11-187O7.3" "MRC1" "ATP6V0D1-DT" "RP11-495L19.1"
## [33] "RP11-437L7.2" "RP11-168F24.3" "RP11-4F5.3" "KCNQ2"
## [37] "HTR1E" "KCNQ5" "RP11-249L21.6"
## $reactome
## category over_represented_pvalue
## 1177 voltage gated potassium channels 3.132597e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 1177 0.9999998 3 7 0.0370273
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8955084 478.3 16112782 860.6 NA 16112782 860.6
## Vcells 16667379 127.2 31295163 238.8 65536 31295163 238.8
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] goseq_1.50.0 geneLenDataBase_1.34.0 BiasedUrn_2.0.10
## [4] fgsea_1.24.0 biomaRt_2.54.1 limma_3.54.2
## [7] tidyr_1.3.0 ggpubr_0.6.0 ggplot2_3.4.2
## [10] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 GenomeInfoDb_1.34.9
## [9] tools_4.2.3 backports_1.4.1
## [11] bslib_0.4.2 utf8_1.2.3
## [13] R6_2.5.1 mgcv_1.8-42
## [15] DBI_1.1.3 BiocGenerics_0.44.0
## [17] colorspace_2.1-0 withr_2.5.0
## [19] tidyselect_1.2.0 prettyunits_1.1.1
## [21] bit_4.0.5 curl_5.0.1
## [23] compiler_4.2.3 cli_3.6.1
## [25] Biobase_2.58.0 xml2_1.3.4
## [27] DelayedArray_0.24.0 rtracklayer_1.58.0
## [29] sass_0.4.5 scales_1.2.1
## [31] rappdirs_0.3.3 Rsamtools_2.14.0
## [33] stringr_1.5.0 digest_0.6.31
## [35] rmarkdown_2.21 XVector_0.38.0
## [37] pkgconfig_2.0.3 htmltools_0.5.5
## [39] MatrixGenerics_1.10.0 dbplyr_2.3.2
## [41] fastmap_1.1.1 rlang_1.1.0
## [43] rstudioapi_0.14 RSQLite_2.3.1
## [45] BiocIO_1.8.0 jquerylib_0.1.4
## [47] generics_0.1.3 jsonlite_1.8.4
## [49] BiocParallel_1.32.6 dplyr_1.1.2
## [51] car_3.1-2 RCurl_1.98-1.12
## [53] magrittr_2.0.3 GO.db_3.16.0
## [55] GenomeInfoDbData_1.2.9 Matrix_1.6-4
## [57] Rcpp_1.0.10 munsell_0.5.0
## [59] S4Vectors_0.36.2 fansi_1.0.4
## [61] abind_1.4-5 lifecycle_1.0.3
## [63] stringi_1.7.12 yaml_2.3.7
## [65] carData_3.0-5 SummarizedExperiment_1.28.0
## [67] zlibbioc_1.44.0 org.Hs.eg.db_3.16.0
## [69] BiocFileCache_2.6.1 grid_4.2.3
## [71] blob_1.2.4 parallel_4.2.3
## [73] crayon_1.5.2 lattice_0.20-45
## [75] splines_4.2.3 Biostrings_2.66.0
## [77] cowplot_1.1.1 GenomicFeatures_1.50.4
## [79] hms_1.1.3 KEGGREST_1.38.0
## [81] knitr_1.44 pillar_1.9.0
## [83] GenomicRanges_1.50.2 rjson_0.2.21
## [85] ggsignif_0.6.4 codetools_0.2-19
## [87] stats4_4.2.3 fastmatch_1.1-3
## [89] XML_3.99-0.14 glue_1.6.2
## [91] evaluate_0.20 png_0.1-8
## [93] vctrs_0.6.2 gtable_0.3.3
## [95] purrr_1.0.1 cachem_1.0.7
## [97] xfun_0.39 broom_1.0.4
## [99] restfulr_0.0.15 rstatix_0.7.2
## [101] tibble_3.2.1 GenomicAlignments_1.34.1
## [103] AnnotationDbi_1.60.2 memoise_2.0.1
## [105] IRanges_2.32.0